When calling a classifier with orange.getProbabilities, I got a list of probabilities. My question is what is the order of the returned probabilities. How can I figure out which prob corresponds to which class?

Probabilites in the list returned by some orange classifier, whengetProbabilities is passed as an argument, are probabilities ofclass values. The order matches the order of a list of values forthe class, which can be obtained by

This implies the user should always consult data.domain.classVar.values to get correct order of the outputed probability because of the way data being loaded.

You're right. But if you would like to always have the same order of class values, list them in your data file. For that, you should use tab-delimited data file, where in the second line instead of using "discrete" for a class value, list the attribute values (separate them with spaces, see http://www.ailab.si/orange/doc/referenc ... imited.htm).